R Notebook
Analysis and visualisation of spatial transcriptomics data. Generally followed this Seurat workflow.
Load libraries
library(Seurat)
library(ggplot2)
library(patchwork)
library(dplyr)
library(UCell)
#library(ggpubr)Load merged liver slices and set identity
sobj <- readRDS("../spatial/merged_spatial_sobj.RDS")
Idents(sobj) <- "SCT_snn_res.0.2"Visualise clusters on spatial plot
plot1 <- SpatialDimPlot(sobj, alpha = 0.7, images = 'slice1') & NoLegend()plot2 <- SpatialDimPlot(sobj, alpha = 0.7, images = 'slice1.1') +
labs(fill = "Cluster")plot1 + plot2
pdf("./figures/spatial/merged_dimPlot_UMAP.pdf")plot1 + plot2
dev.off()png
2 
Visualise features on spatial plot
Calculate markers
all.markers <- FindAllMarkers(sobj,
only.pos = TRUE,
min.pct = 0.25,
logfc.threshold = 0.25,
recorrect_umi = FALSE)
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|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=01s top.markers <- all.markers %>% group_by(cluster) %>% top_n(n = 10, wt = avg_log2FC)
top.markersCreate zonation scores using top 10 genes from periportal and pericentral clusters
# Compare clusters 0 and 1
markers <- FindMarkers(sobj,
ident.1 = '0',
ident.2 = '1',
only.pos = FALSE,
min.pct = 0.25,
logfc.threshold = 0.25,
recorrect_umi = FALSE)
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markers <- markers[grep("mikado", rownames(markers), invert = TRUE),]
# Get top 30 periportal genes
pp_genes <- rownames(markers[markers$avg_log2FC > 0,])[1:10]
pp_genes [1] "Saa2;Saa1-1" "HAMP"
[3] "APOA1" "APOC2"
[5] "CRYL1" "AMY1A;AMY1C;AMY1B;AMY2A;AMY2B"
[7] "MT-ATP6" "UROC1"
[9] "APOA2" "MT-CO3" # Get top 30 pericentral genes
cv_genes <- rownames(markers[markers$avg_log2FC < 0,])[1:10]
cv_genes [1] "FETUB" "HMGCS1" "CYP2E1" "GLUD1;GLUD2" "CYP1A2" "RGN"
[7] "INMT" "COMT" "FDPS" "SPR-1" Format for UCell
mySigs <- list()
mySigs$Periportal <- pp_genes
mySigs$Pericentral <- cv_genes
mySigs$Periportal
[1] "Saa2;Saa1-1" "HAMP"
[3] "APOA1" "APOC2"
[5] "CRYL1" "AMY1A;AMY1C;AMY1B;AMY2A;AMY2B"
[7] "MT-ATP6" "UROC1"
[9] "APOA2" "MT-CO3"
$Pericentral
[1] "FETUB" "HMGCS1" "CYP2E1" "GLUD1;GLUD2" "CYP1A2" "RGN"
[7] "INMT" "COMT" "FDPS" "SPR-1" Add these as gene signatures
sobj <- AddModuleScore_UCell(sobj, features = mySigs, assay = "SCT")
signature.names <- paste0(names(mySigs), "_UCell")
VlnPlot(sobj, features = signature.names, group.by = "SCT_snn_res.0.2")
SpatialFeaturePlot(sobj,
features = signature.names,
images = 'slice1')
SpatialFeaturePlot(sobj,
features = signature.names,
images = 'slice1.1')
Create figures of spatial plots with signatures
plot1 <- SpatialFeaturePlot(sobj,
features = "Periportal_UCell",
images = 'slice1')plot2 <- SpatialFeaturePlot(sobj,
features = "Periportal_UCell",
images = 'slice1.1')pdf("./figures/spatial/periportalSig_spatial_UCell.pdf")
plot1 + plot2
dev.off()null device
1 plot1 <- SpatialFeaturePlot(sobj,
features = "Pericentral_UCell",
images = 'slice1')plot2 <- SpatialFeaturePlot(sobj,
features = "Pericentral_UCell",
images = 'slice1.1')pdf("./figures/spatial/pericentralSig_spatial_UCell.pdf")
plot1 + plot2
dev.off()null device
1 Create heatmap with signature genes
Correlate UMAP zonation scores with gene expression
FeaturePlot(sobj, features = c("WNT2", "Pericentral_UCell"), blend = TRUE)Warning: Could not find WNT2 in the default search locations, found in ‘Spatial’ assay instead
FeatureScatter(sobj, feature1 = "WNT2", feature2 = "Pericentral_UCell")Warning: Could not find WNT2 in the default search locations, found in ‘Spatial’ assay instead
Calculate Z-score for each gene for CV and PP signatures
zscore = (sobj@assays$SCT@scale.data['CYP2E1',] - sobj$Pericentral_UCell)/sd(sobj$Pericentral_UCell)
sobj$cyp2e1_zscore <- scale(zscore)
SpatialFeaturePlot(sobj, features = 'cyp2e1_zscore', images = 'slice1')
Try with RSPO3
zscore = (sobj@assays$SCT@scale.data['RSPO3',] - sobj$Pericentral_UCell)/sd(sobj$Pericentral_UCell)
sobj$rspo3_zscore <- scale(zscore)
SpatialFeaturePlot(sobj, features = 'rspo3_zscore', images = 'slice1')
Correlate all genes with CV and PP signatures
cv_cor <- apply(sobj@assays$SCT@counts, 1, function (x) cor(x, y = sobj$Pericentral_UCell,
method = "spearman"))Warning: the standard deviation is zerohead(sort(cv_cor, decreasing = TRUE)) FETUB CYP2E1 HMGCS1 CYP1A2 RGN COMT
0.7660823 0.7393928 0.7129019 0.6500996 0.6442300 0.6336671 pp_cor <- apply(sobj@assays$SCT@counts, 1, function (x) cor(x, y = sobj$Periportal_UCell,
method = "spearman"))Warning: the standard deviation is zerohead(sort(pp_cor, decreasing = TRUE)) HAMP Saa2;Saa1-1 AMY1A;AMY1C;AMY1B;AMY2A;AMY2B
0.7191834 0.6434277 0.5996466
APOA1 CRYL1 APOC2
0.5084247 0.5080673 0.5008200 Write table
spatial_cors <- cbind(cv_cor, pp_cor)
write.table(spatial_cors,
file = "./figures/spatial/spatial_gene_correlations.tsv",
quote = FALSE,
sep = "\t",
row.names = TRUE,
col.names = TRUE)Save object if needed
saveRDS(sobj,
file = "../spatial/merged_spatial_sobj.RDS")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